DNA, Volume 6, Issue 2 (June 2026) – 14 articles

Eosinophilic esophagitis (EoE) and inflammatory bowel disease (IBD) are immune-mediated disorders of the gastrointestinal (GI) tract that, despite involving different tissues, are increasingly recognized to coexist. Epidemiologic studies demonstrate a bidirectional association, with patients affected by one condition showing a higher-than-expected prevalence of the other, suggesting shared susceptibility rather than incidental overlap. Genetic and epigenetic data support partial convergence in immune regulatory pathways, while epithelial barrier dysfunction and antigen-driven immune activation emerge as common upstream features. Overlapping cytokine networks, including IL-4, IL-13, and IL-23 signaling, contribute to chronic inflammation in both diseases, although differences in tissue environment and immune dominance give rise to distinct inflammatory phenotypes and clinical behavior. Clinical outcomes in patients with dual diagnoses appear heterogeneous, with available data suggesting neither uniformly worsened nor clearly protective disease courses, underscoring the complexity of shared immune mechanisms operating within different anatomic contexts. Beyond inflammatory activity, coexistence of EoE and IBD poses important nutritional and quality-of-life challenges, as overlapping dietary restrictions and chronic symptoms increase the risk of malnutrition, micronutrient deficiencies, and psychosocial burden. Current therapies remain disease-specific, with strong evidence supporting proton pump inhibitors, swallowed topical steroids, dietary therapy, and dupilumab in EoE, and biologics and small molecules targeting TNF-α, IL-12/23, IL-23, integrins, and JAK–STAT signaling in IBD, while evidence guiding treatment in patients with dual diagnosis remains limited. Together, current evidence supports a framework of shared immune machinery with tissue-specific expression that explains coexistence while preserving the distinct identities of EoE and IBD. By integrating emerging genetic, immunologic, and clinical evidence, this review aims to provide a framework for understanding and managing patients with coexisting EoE and IBD. Full article

Introduction: Does DNA superhelicity effect nucleic acid interactions with drugs? To test such a possibility, the interactions of the linear and superhelical forms of the pGEX-4T-2 plasmid have been investigated with a newly synthesized compound, 4-chloro-6-(1H-imidazo [4,5-b]phenazine-2-yl)benzene-1,3-diol, positively tested for the antiproliferative (cell growth-limiting) properties, important for the development of anticancer drugs. Methods: The accumulation of the compound, and its possible reorientation (phase transition) within the plasmid layer adsorbed on a Glassy Carbon (GC) electrode has been monitored in 5 min. intervals using alternatively two voltammetric methods—Differential Pulse (DP), showing redox properties and—Alternating Current (AC), reflecting both redox and structural properties (capacity/resistance change related to DNA condensation) of the DNA-drug layers. Results and Discussion: The accumulation plots of the compound in plasmid layers are different for superhelical and linear pGEX-4T-2 and also depend on the DNA coverage by the compound. The reorientation (phase transition) occurs at a compound concentration 2 µM for the superhelical plasmid and 1.5 µM for the linear one, as compared to 8 µM for the compound layer formed on bare GC, thus proving the existence of the DNA–compound interactions. Interestingly, the phase transition is redox-sensitive, e.g., AC redox signal II is visible for the linear, but not for the superhelical plasmid, thus reflecting different orientation of the compound in these two types of pGEX-4T-2 plasmid, related to the condensation in the DNA–compound layer and seen as a decrease in the C/R signal. Conclusions: The results suggest that the reorientation of the compound leading to plasmid condensation occurs differently in supercoiled and linear pGEX-4T-2 (redox specific accumulation and condensation). Full article

Liquid biopsy has evolved beyond its original role as a minimally invasive approach for mutation detection and is now being developed as a broader analytical framework for cancer detection, stratification, and longitudinal monitoring. Improvements in next-generation sequencing, assay chemistry, and computational analysis have increased analytical sensitivity, including in settings with low tumor fraction and very low variant allele abundance. These advances have expanded the utility of cfDNA analysis in measurable residual disease assessment and in the detection of low-abundance tumor-derived signals across multiple clinical contexts. At the same time, the field has shifted toward interpreting cfDNA as a carrier of higher-order biological information rather than solely a substrate for mutation calling. Fragmentation profiles, nucleosome positioning, and chromatin accessibility patterns derived from plasma DNA have been used to infer transcriptional and regulatory states, raising the possibility that cfDNA may capture functional tumor states not readily accessible through genotype-focused assays alone. These developments have prompted growing interest in chromatin-informed cfDNA analysis as a means of identifying pathway activity, enhancer usage, transcription factor occupancy, and potentially actionable biological dependencies. However, the translational relevance of many such inferences remains incompletely established, and preanalytical variability, limited cross-cohort generalizability, and the gap between analytical performance and clinical utility continue to constrain clinical translation. This review examines the role of cfDNA in adaptive oncology, highlighting recent analytical advances, assessing the current evidence supporting their biological and clinical utility, and considering the extent to which cfDNA-derived regulatory inference may contribute to adaptive oncology and therapeutic decision-making. Full article

Background/Objectives: Multiplex and point-of-care (POC) diagnostics require each probe to detect one intended target while rejecting many closely related sequences under shared room-temperature conditions. The conventional focus on mismatch count is incomplete: two alignments with the same number of matches and mismatches can have very different off-target risks depending on whether mismatches are clustered or distributed. We introduce a simple visual heuristic that scores mismatch placement rather than mismatch count alone. Methods: Effective complementary island (ECI) score retained matched continuity after subtracting one base for each mismatch- or gap-exposed edge. The score is S_ECI = Σ_i ECI_i^2, and the design margin is ΔS_ECI = S_ECI (intended) − S_ECI (highest-scoring non-intended alignment by ECI). ECI is not a thermodynamic model; thermodynamics (ΔG37) is used separately to verify an adequate sensitivity floor. We retrospectively applied ECI to a fixed 39-target HPV capture-probe benchmark and to a public Affymetrix dataset contrasting clustered versus distributed mismatches at identical or near-identical mismatch counts. Results: In the HPV benchmark, ECI separated intended from off-target in 32/39 panels; ΔG37 favored the intended duplex in 31/39 panels; both layers were concordant in 36/39 panels. In the Affymetrix dataset (n = 8 probes, 2–4 mismatches), S_ECI correlated with reported log2 hybridization intensity (Pearson r = 0.92, p = 0.0014). Within the strict three-mismatch subset (n = 5), S_ECI remained correlated with intensity (r = 0.96; p = 0.010), while ΔG37 was uncorrelated (r = −0.04; p = 0.95), supporting the narrower claim that mismatch placement can affect signal even when mismatch count is fixed. Conclusions: ECI is not a replacement for thermodynamics, BLAST, target-accessibility analysis, empirical optimization, or machine-learning prediction. It adds one actionable readout: where to shift, shorten, or place a limited intentional mismatch so that intended retained continuity stays above the assay floor while the highest-scoring off-target island by ECI is fragmented. We provide a bench-ready workflow for multiplex, room-temperature, and POC probe design. Full article

Background/Objectives: Chromosome research is essential for advancing our understanding of cytogenetics, gene regulation and numerous aspects of organismal health. Staining chromosomes with 4′,6-diamidino-2-phenylindole (DAPI) and applying Fluorescence Lifetime Imaging Microscopy (FLIM) enables the assessment of structural changes in pericentromeric and heterochromatin-rich region of chromosomes 1, with a shorter fluorescence lifetime (FLT) in the pericentromeric regions compared to the arms. Methods: We used FLIM to optimise sample preparation conditions for more robust imaging and furthermore to measure the impact of low-dose X-ray ionising radiation on chromosome structure when labelled with DAPI. Results: We applied this method to different DNA stains bound to chromosomes where only DAPI led to a clear FLT difference between the chromosome arms (p,q) with 2.98 ± 0.12 ns and 2.65 ± 0.07 ns at the pericentromeric region, while similar stains, such as Hoechst 33258 and NucBlue^TM did not highlight these regions as clearly following FLIM analysis. Our data showed that chromosomes of cells irradiated with 0.1 Gy and 1 Gy did not show a significant change in FLTs (2.94 ± 0.09 ns on the arms and 2.60 ± 0.06 ns on the pericentromeric region) of chromosome 1. Whilst irradiation with 0.5 Gy led to a noticeable and significant reduction in FLT with 2.42 ± 0.13 ns on the arms and 2.12 ± 0.06 ns on the pericentromeric region of HeLa chromosomes. The same pattern could also be seen on X-ray-irradiated T-cell chromosomes. Conclusions: These findings indicate that DAPI FLT may be a useful tool to measure chromosomal structural changes and further suggests that chromosomes undergo distinct structural changes at the pericentromeric region following low-dose irradiation. Full article

Cancer cells have many derailed processes due to which they have a higher proliferative capacity. The rewiring is continuously taking place to meet their metabolic demands. The demands depend on the stage of cancer, and these differences create challenges in curing them. Nucleotide metabolism plays a pivotal role in shaping cancer fate. DNA repair and other damage pathways also play a key role in cancer progression, genomic instability, errors in genetic material etc. These are discussed in this mini review so that researchers can take the lead to make an effort to combat cancer and design new therapeutics. Full article

Background: Long non-coding RNAs (lncRNAs) are increasingly recognized as key regulators of gene expression, playing pivotal roles in diverse biological processes, including reproduction. This study identified and characterized lncRNAs located near fertility-associated genes in Retinta beef cattle, exploring their potential regulatory roles via DNA–RNA triplex formation using in silico approaches. Methods: We applied an integrative bioinformatics pipeline to identify potential triplex interactions, predicting structurally accessible regions within the lncRNAs and demonstrating the statistical enrichment of binding sites across known regulatory genomic elements. Results: Twelve protein-coding genes previously linked to female fertility or male scrotal circumference were analyzed, revealing 16 unique lncRNAs within ±50 kb windows, predominantly on BTA5. We predicted high-confidence triplex-forming oligonucleotides (TFOs) for most gene-lncRNA pairs. Our results suggest robustness and sequence specificity, as interactions were disrupted by sequence permutation or when a control background sequence was used. RNA secondary-structure analysis revealed that TFOs generally lie in exposed regions, supporting their accessibility for triplex formation. Furthermore, promoter and regulatory regions of fertility-associated genes were enriched in predicted triplex target sites (TTSs), with some overlapping CpG islands and enhancer regions, leading to the hypothesis that these lncRNAs might play a role in epigenetic regulation. Conclusions: Overall, these findings establish computationally derived hypotheses regarding the potential molecular mechanisms by which lncRNAs may modulate reproductive efficiency in cattle and highlight specific lncRNAs as promising targets for functional studies and marker-assisted breeding. Full article

Real-time selective sequencing on nanopore platforms offers a programmable way to enrich target molecules and deplete background DNA during a run. This approach, widely known as adaptive sampling (AS), has been applied across host depletion, metagenomics, targeted loci, plasmid/AMR workflows, and RNA/transcriptomic protocols, but reported performance varies substantially across studies. This review synthesizes current algorithmic and empirical evidence with emphasis on sequencing-relevant outcomes, including absolute informative yield, target-coverage behavior, throughput effects, and run-to-run stability. Across use cases, relative enrichment is frequently observed, but gains in usable genomic output are strongly conditioned by fragment-length distributions, reference quality, decision-loop latency, and rejection-associated penalties in total yield and pore longevity. Evidence from targeted-panel and complex-locus studies further indicates that improved depth concentration can coexist with coverage non-uniformity and context-specific trade-offs relative to wet-lab enrichment. Overall, the literature supports AS as a valuable but condition-dependent strategy whose benefit is greatest when assay design, reference selection, and computational constraints are jointly optimized. Full article

Epigenetics is a widely present mechanism for the modulation of gene expression without alterations in the underlying genetic sequence. Epigenetic signatures are significantly present in bacteria, with DNA methylation playing a key role in the modulation of bacterial physiology and pathogenesis. DNA methyltransferases (MTases) are the enzymes catalyzing the transfer of methyl groups to adenine or cytosine residues in the DNA using the methyl donor S-adenosyl-L-methionine (SAM). This process generates modified bases, N6-methyladenine (m6A), 5-methylcytosine (5mC), or N4-methyl cytosine (4mC) in the DNA, which influence fundamental cellular processes such as DNA transactions, DNA replication, transcription, and DNA repair. These MTases, earlier thought to be a part of primitive bacterial immune system, are now considered to be active players in gene regulation. They regulate bacterial adaptability to stress by virtue of phase variation and bistability. In pathogenic species such as Mycobacterium tuberculosis (Mtb), DNA methylation driven epigenetic reprogramming influences the expression of virulence factors, antibiotic tolerance, and persistence genes. This review gives a detailed account of role of DNA methyltransferases in bacterial epigenomics influencing various cellular processes. With the development of long-read high-throughput sequencing technologies, single-base mapping of bacterial methylomes has become possible. In the latter part of the review, we talk about these advances and the integration of synthetic biology to expand the potential of methylation systems for developing biosensors and switchable gene expression platforms. These strategies can be translated into future vaccine design and precision drugs for disease control. Deciphering bacterial DNA methylation can help gain insights into microbial evolution and design innovative therapeutics for various diseases. Full article

Background: Piper is one of the largest genera in the family Piperaceae, with approximately 2100 species. Most Piper species are used as spices or as medicinal plants. Piper methysticum G. Forst., popularly known as kava-kava (or kava), is widely used to treat anxiety disorders. Due to similar morphological features, P. auritum Kunth (known as “false kava”) is sometimes mistakenly or intentionally used as an alternative botanical source for “kava” extracts. The false kava extracts do not contain active kavalactones but contain safrole, which is hepatotoxic. It is important to verify the component botanical materials in order to evaluate the quality and safety attributes of a potential botanical drug. Some studies have evaluated genetic variation in Piper sp. using the chloroplast regions matK, rbcL, rpoC1 and trnH-psbA and the nuclear ITS2 markers. However, none has focused on the identification of P. methysticum using DNA barcodes. In the present investigation, the ITS2 DNA barcode region from the nuclear genome was tested to confirm the identification and authentication of kava-kava samples. Methods: Seven P. methysticum samples were collected from three different geographic lo-cations and two P. auritum samples were collected and the ITS2 region from the nuclear genome, was amplified, sequenced and aligned to determine their genetic distances. Results: The ITS2 locus showed high amplification and sequence output with a discriminating barcode gap. A distance-based phylogenetic tree and BLAST confirmation (using blastn) revealed the ITS2 locus as a diagnostic DNA barcode for the accurate identification of kava-kava species. Discussion: In conclusion, the ITS2 region proves to be an effective and reliable DNA barcode for distinguishing P. methysticum from closely related species such as P. auritum. Its application can significantly improve the safety, quality, and traceability of kava-containing products, addressing a critical need in the standardization of botanical drugs. Full article

Lodgepole pine (Pinus contorta Dougl.) exhibits pronounced morphological variation across its range, historically attributed to allopatric differentiation during the Wisconsin glaciation. However, whether genetic divergence aligns with morphological differentiation—a fundamental prediction of allopatric speciation theory—remains untested. We conducted a comprehensive phylogeographic analysis of chloroplast DNA (trnL intron and trnL/trnF spacer) and mitochondrial DNA (nad1 b/c intron) across 31 populations representing all four recognized subspecies to test hypotheses of refugial isolation and to evaluate the genetic basis of current taxonomic classification. Contrary to predictions of allopatric divergence, both organellar genomes showed striking genetic uniformity (π = 0.000178–0.000186; intersubspecific genetic distances: 1.06 × 10⁻⁴ to 3.96 × 10⁻⁴) with no phylogenetic structure corresponding to morphological boundaries. Significant negative neutrality test values (Tajima’s D = −2.26, p < 0.02; Fu and Li’s D* = −4.52, p < 0.02) suggest recent demographic expansion rather than equilibrium divergence. A distinctive 5 bp indel in coastal populations provides molecular evidence for a northern Pacific refugium, and its occurrence in interior populations is consistent with post-glacial pollen-mediated gene flow, though this directionality remains inferential pending nuclear genomic confirmation. These findings suggest that morphological divergence reflects rapid adaptive evolution in heterogeneous environments rather than deep phylogenetic divisions. This pattern exemplifies gene flow-selection balance, in which divergent selection maintains local adaptation despite extensive gene flow—supporting an ecotypic rather than a phylogenetic interpretation of intraspecific diversity. The persistence of morphological variation despite genetic homogeneity indicates strong selection on ecologically important traits, likely driven by variation in fire regimes, differential seed predation, and climate gradients. These results have critical implications for understanding adaptive evolution rates in widespread conifers and for developing conservation strategies that emphasize adaptive processes over taxonomic categories. Full article

Recombinogenic DNA damage can initiate chromosomal rearrangements that can alter gene expression or accelerate cancer progression in higher eukaryotes. Thus, there is a critical need to identify genes that suppress chromosomal rearrangements and environmental exposures that promote genetic instability. Cell cycle checkpoints modulate the cell cycle so that DNA repair occurs before the replication or segregation of damaged chromosomes. Saccharomyces cerevisiae (budding yeast) RAD9 was the first cell cycle checkpoint gene identified, which initiated intensive research studies into the mechanisms of checkpoint activation and the phenotypes of checkpoint mutants. The budding yeast Rad9 protein serves as both an adaptor and scaffold that facilitates downstream effector activation to orchestrate a DNA damage response at multiple stages of the cell cycle, which facilitates double-strand break (DSB) repair by sister chromatid recombination. However, the role of RAD9 in homologous recombination and in suppressing gross chromosomal rearrangements (GCRs) is not completely understood. In this review we discuss how RAD9 can promote genome instability resulting from aberrant DNA replication intermediates, while suppressing DSB-associated rearrangements. We also discuss possible mechanisms accounting for the synergistic increase in genomic instability in double mutants defective in both RAD9 and recombinational repair. We emphasize that while there is an overlap between checkpoint and recombinational repair pathways, RAD9 and checkpoint pathways can function independently to suppress chromosomal instability. These studies thus elucidate checkpoint mechanisms that control homologous recombination between repeated sequences. Full article

Gut dysbiosis, defined as a disruption in the structure or function of the intestinal microbiota, is increasingly recognized as a key contributor to inflammatory, metabolic, and neuropsychiatric diseases. Conventional interventions such as broad-spectrum antibiotics, generic probiotics, and fecal microbiota transplantation (FMT) often show limited and inconsistent efficacy because they lack specificity, durability, and robust safety controls. In contrast, recent advances in DNA-based technologies are reshaping the therapeutic landscape by enabling targeted, programmable, and mechanistically informed modulation of the gut ecosystem. This review presents an integrated overview of three major domains driving this shift: CRISPR-based systems that selectively delete, silence, or reprogram microbial genes; synthetic biology-driven live therapeutics engineered to sense disease-associated cues and execute controlled responses; and metagenomics-informed strategies that tailor interventions to patient-specific microbial gene profiles and functional deficits. Additionally, we examine the continued evolution of FMT toward DNA-optimized workflows and defined microbial consortia that offer safer, more standardized alternatives to crude donor material. Across these domains, we discuss delivery platforms (including bacteriophages, conjugative plasmids, extracellular vesicles, and synthetic nanoparticles), and compare their efficiency, specificity, and scalability. We further highlight how DNA-guided interventions interface with host immunity—shaping Treg/Th17 balance, mucosal barrier function, and inflammatory signaling—while also analyzing ecological and evolutionary risks, biocontainment strategies, and regulatory classification gaps that will govern clinical translation. Together, these developments signal a transition from empirical microbiome manipulation to rational ecosystem engineering. DNA-guided therapies hold strong promise for precise and personalized management of gut-related diseases, but their success will depend on rigorous ecological risk assessment, long-term monitoring, and adaptive regulatory frameworks alongside continued technological innovation. Full article

Background/Objectives: Exposure of cells to ionizing radiation induces isolated DNA lesions, including single-strand breaks, apurinic/apyrimidinic sites, and oxidized bases, as well as clustered damages of different complexity. The latter types of damage are difficult to repair, and the failure to process them accurately and efficiently is related to the induction of mutagenesis, genomic instability, cancer, and aging. Since various types of clustered lesions may occur simultaneously after radiation exposure, leading to a complex architecture of DNA damage, the study of the concomitant formation and the removal kinetics of clustered DNA damage is important to determine the mutagenic and, consequently, the carcinogenic potential of ionizing radiation. Methods: With the aim of capturing real-time coexisting lesion types and assessing the repair kinetics of clustered damages, the simultaneous determination of double-strand breaks, apurinic/apyrimidinic site clusters, and oxypurine clusters induced by γ-irradiation of Saccharomyces cerevisiae yeast cells was performed immediately after exposure and at time intervals during incubation in Liquid Holding Recovery conditions. Results: Ionizing radiation induced lethal and mutagenic events, leading to a dose-dependent linear increase in double-strand breaks, apurinic/apyrimidinic site clusters, and oxypurine clusters. The kinetic study showed that double-strand break frequencies declined during Liquid Holding Recovery, although a transient increase was detected at early time points. At 160 Gy, apurinic/apyrimidinic site clusters repair was evident, whereas at 400 Gy the frequency of damage increased before returning to the initial value at 24 h. In contrast, oxypurine clusters showed no net increase in repaired lesions over 24 h. Conclusions: The complex nature and topological characteristics of ionizing radiation-induced clustered DNA damage may influence lesion processing. Also, ionizing radiation may disrupt redox cellular homeostasis, leading to DNA damage and delayed effects. Full article